Biology subjects

Gurry, T.

Publications and source records attributed to Gurry, T..

3 recordsLinked to original sources

bioRxiv2017

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here, we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.

microbiology↗

bioRxiv2017

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a hosts microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patients microbiota.

microbiology↗

bioRxiv2017

Meta Analysis Of Microbiome Studies Identifies Shared And Disease-Specific Patterns

1Hundreds of clinical studies have been published that demonstrate associations between the human microbiome and a variety of diseases. Yet, fundamental questions remain on how we can generalize this knowledge. For example, if diseases are mainly characterized by a small number of pathogenic species, then new targeted antimicrobial therapies may be called for. Alternatively, if diseases are characterized by a lack of healthy commensal bacteria, then new probiotic therapies might be a better option. Results from individual studies, however, can be inconsistent or in conflict, and comparing published data is further complicated by the lack of standard processing and analysis methods.\n\nHere, we introduce the MicrobiomeHD database, which includes 29 published case-control gut microbiome studies spanning ten different diseases. Using standardized data processing and analyses, we perform a comprehensive crossdisease meta-analysis of these studies. We find consistent and specific patterns of disease-associated microbiome changes. A few diseases are associated with many individual bacterial associations, while most show only around 20 genus-level changes. Some diseases are marked by the presence of pathogenic microbes whereas others are characterized by a depletion of health-associated bacteria. Furthermore, over 60% of microbes associated with individual diseases fall into a set of \"core\" health and disease-associated microbes, which are associated with multiple disease states. This suggests a universal microbial response to disease.

microbiology↗